A New Method for Standardizing Inland Fish Community Surveys: Characterizing Habitat Associated with Small-Bodied Fish Species, Abundance, and Size Distributions in a Highly Modified Estuary

Monitoring fish assemblages in estuary environments is often difficult to standardize due to habitat complexity and gear-specific selectivity. This is further compounded by conventional sampling methods which require fish handling that might cause stress or mortality. To ameliorate these issues, we developed the Single-Platform Aquatic Species and Habitat Sampling System (Platform), an integrated and mobile concentrator net and live box prototype, coupled with a range of physical monitoring equipment. The long-term goal of the Platform is to employ non-invasive sampling techniques such as video and eDNA; however, our aim in this study was to test the Platform’s ability to sample across different habitat types and detect differences in fish assemblages. We investigated the utility of the Platform over a short time period (2 mo) in a relatively small and complex embayment within the highly modified San Francisco Estuary, California. We were able to identify clear physical distinctions among estuary/delta habitat types and detect habitat segregation by ecological groups of sampled fishes with the Platform. The Platform also detected discernable ontogenetic shifts (i.e., size differences) within estuary habitats of commonly observed fish species. These initial results demonstrate the Platform’s ability to contrast fish density, size, and species diversity, which sets the stage to advance more passive monitoring techniques, including video and eDNA methods. The Platform has the potential to fill a methodological gap in non-invasive surveying of small-bodied fish across a range of estuarine habitats, warranting further investigation of potential applications